Broad Fungal Genomics group scripts
This repository hosts scripts used publications to carry out fungal genomic analyses.
Usage example:
filterGatkGenotypes.py --min_GQ 50 --min_percent_alt_in_AD 0.8 --min_total_DP 10 ${VCF} > ${FILTERED_VCF} 2> variant_qc_genotype_filter.tsv
Usage example:
python vcfSnpsToFasta.py --max_amb_samples 40 list_vcf > filtered.SNPs.fa
Usage example:
python vcfSnpsToGeneFasta.py list_of_vcf_files reference.fasta reference.gff gene_id > output.fasta